Cy0: Cy0 alternative to threshold cycles as in Guescini et al....

In qpcR: Modelling and Analysis of Real-Time PCR Data

Description

An alternative to the classical crossing point/threshold cycle estimation as described in Guescini et al (2002). A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and the intersection with the x-axis is calculated.

Usage

Cy0(object, plot = FALSE, add = FALSE, ...)

Arguments

object	a fitted object of class 'pcrfit'.
plot	if TRUE, displays a plot of Cy0.
add	if TRUE, a plot is added to any other existing plot, i.e. as from plot.pcrfit.
...	other parameters to be passed to plot.pcrfit or points.

Details

The function calculates the first derivative maximum (cpD1) of the curve and the slope and fluorescence F_{cpD2} at that point. Cy0 is then calculated by Cy_0 = cpD1 - \frac{F_{cpD2}}{slope}.

Value

The Cy_0 value.

Author(s)

Andrej-Nikolai Spiess

References

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition.
Guescini M, Sisti D, Rocchi MB, Stocchi L & Stocchi V.
BMC Bioinformatics (2008), 9: 326.

Examples

## Single curve with plot.
m1 <- pcrfit(reps, 1, 2, l5)
Cy0(m1, plot = TRUE)

## Add to 'efficiency' plot.
efficiency(m1)
Cy0(m1, add = TRUE)

## Compare s.d. of replicates between
## Cy0 and cpD2 method. cpD2 wins!
ml1 <- modlist(reps, model = l4)
cy0 <- sapply(ml1, function(x) Cy0(x))
cpd2 <- sapply(ml1, function(x) efficiency(x, plot = FALSE)$cpD2)
tapply(cy0, gl(7, 4), function(x) sd(x))
tapply(cpd2, gl(7, 4), function(x) sd(x)) 

Example output

Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase
Loading required package: Matrix
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
[1] "pcrfit" "nls"   
[1] 14.69
[1] "pcrfit" "nls"   
$eff
[1] 1.7947

$resVar
[1] 0.00603899

$AICc
[1] -103.189

$AIC
[1] -104.5843

$Rsq
[1] 0.9997843

$Rsq.ad
[1] 0.9997647

$cpD1
[1] 17.59

$cpD2
[1] 15.68

$cpE
[1] NA

$cpR
[1] NA

$cpT
[1] NA

$Cy0
[1] NA

$cpCQ
[1] NA

$cpMR
[1] NA

$fluo
[1] 2.356366

$init1
[1] 0.03706216

$init2
[1] 0.0002452738

$cf
[1] NA

[1] 14.69
Making model for F1.1 (l4)
 => Fitting passed...

Making model for F1.2 (l4)
 => Fitting passed...

Making model for F1.3 (l4)
 => Fitting passed...

Making model for F1.4 (l4)
 => Fitting passed...

Making model for F2.1 (l4)
 => Fitting passed...

Making model for F2.2 (l4)
 => Fitting passed...

Making model for F2.3 (l4)
 => Fitting passed...

Making model for F2.4 (l4)
 => Fitting passed...

Making model for F3.1 (l4)
 => Fitting passed...

Making model for F3.2 (l4)
 => Fitting passed...

Making model for F3.3 (l4)
 => Fitting passed...

Making model for F3.4 (l4)
 => Fitting passed...

Making model for F4.1 (l4)
 => Fitting passed...

Making model for F4.2 (l4)
 => Fitting passed...

Making model for F4.3 (l4)
 => Fitting passed...

Making model for F4.4 (l4)
 => Fitting passed...

Making model for F5.1 (l4)
 => Fitting passed...

Making model for F5.2 (l4)
 => Fitting passed...

Making model for F5.3 (l4)
 => Fitting passed...

Making model for F5.4 (l4)
 => Fitting passed...

Making model for F6.1 (l4)
 => Fitting passed...

Making model for F6.2 (l4)
 => Fitting passed...

Making model for F6.3 (l4)
 => Fitting passed...

Making model for F6.4 (l4)
 => Fitting passed...

Making model for F7.1 (l4)
 => Fitting passed...

Making model for F7.2 (l4)
 => Fitting passed...

Making model for F7.3 (l4)
 => Fitting passed...

Making model for F7.4 (l4)
 => Fitting passed...

Calculating delta of first/second derivative maxima...
.........10.........20........
        1         2         3         4         5         6         7 
0.3742103 0.8725203 0.7402421 0.4555857 0.3611440 0.2259056 0.3792427 
         1          2          3          4          5          6          7 
0.26961392 0.75185881 0.57402091 0.30155154 0.14863266 0.06551081 0.29803523 

qpcR documentation built on May 2, 2019, 5:17 a.m.